Published January 13, 2014
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DNA replication and spindle checkpoints cooperate
during S phase to delay mitosis and preserve
genome integrity
Maria M. Magiera, Elisabeth Gueydon, and Etienne Schwob
D
eoxyribonucleic acid (DNA) replication and chro­
mosome segregation must occur in ordered seq­
uence to maintain genome integrity during cell
proliferation. Checkpoint mechanisms delay mitosis
when DNA is damaged or upon replication stress, but
little is known on the coupling of S and M phases in
unperturbed conditions. To address this issue, we post­
poned replication onset in budding yeast so that DNA
synthesis is still underway when cells should enter mitosis.
This delayed mitotic entry and progression by transient
activation of the S phase, G2/M, and spindle assembly
checkpoints. Disabling both Mec1/ATR- and Mad2dependent controls caused lethality in cells with deferred
S phase, accompanied by Rad52 foci and chromosome
missegregation. Thus, in contrast to acute replication
stress that triggers a sustained Mec1/ATR response, mul­
tiple pathways cooperate to restrain mitosis transiently
when replication forks progress unhindered. We sug­
gest that these surveillance mechanisms arose when both
S and M phases were coincidently set into motion by a
unique ancestral cyclin–Cdk1 complex.
Introduction
Maintenance of genome integrity depends on the successful
completion of several cellular events, the most prominent being
genome duplication during S phase and chromosome segregation in mitosis. These key cell cycle events are orchestrated in all
eukaryotes by waves of Cdk activity. In yeast, three G1 cyclins
(Cln1–3), two B-type cyclins (Clb5,6), and four mitotic cyclins
(Clb1–4) associate with a single catalytic subunit (Cdc28/Cdk1)
to promote start, S phase, and mitosis, respectively (Nasmyth,
1996). Interestingly, a single monomolecular Cdk module suffices for fission yeast proliferation, raising the question of how
the order between S phase and mitosis is maintained (Coudreuse
and Nurse, 2010). Exogenous stress or cell cycle defects trigger
cellular surveillance mechanisms (checkpoints), which delay
cell cycle progression until the problem is resolved (Weinert
and Hartwell, 1988). Mechanisms governing cell cycle progression and monitoring its accuracy are often defective in cancer
Correspondence to Etienne Schwob: [email protected]
M.M. Magiera’s present address is Institut Curie, Centre Universitaire, 91405
Orsay, France.
Abbreviations used in this paper: APC, anaphase-promoting complex; CEN,
centromere; DDK, Dbf4-dependent kinase; DDR, DNA damage response; EdU,
ethynyl-deoxyuridine; HU, hydroxy-urea; KBB, kinase breakage buffer; SAC,
spindle assembly checkpoint; SC, synthetic complete; SPB, spindle pole body;
TetR, tetracycline repressor.
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J. Cell Biol. Vol. 204 No. 2 165–175
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and have therefore been studied extensively (Bartek and Lukas,
2007; Malumbres and Barbacid, 2009).
Chromosome replication is set up in late M-G1 by formation of prereplication complexes made of Orc1–6, Cdc6, Cdt1,
and Mcm2–7 proteins on future sites of bidirectional DNA synthesis called origins (Raghuraman et al., 2001; McGuffee et al.,
2013). At G1/S, S-phase Cdk (Clb5,6–Cdk1) and Dbf4-dependent
kinase (DDK; Dbf4–Cdc7) become active and phosphorylate
several proteins required or DNA replication initiation (Labib,
2010; Tanaka and Araki, 2010). DNA synthesis starts at a subset
of these origins and continues throughout S phase according
to a spatiotemporal replication program that is influenced by
chromatin context, subnuclear localization, the availability of
limiting initiation factors, and checkpoint controls (Raghuraman
et al., 2001; Zegerman and Diffley, 2010; Aparicio, 2013). Completion of DNA replication is key to genome integrity, as incompletely replicated chromosomes fail to segregate correctly
and may break during mitosis. However, because origin firing is
partly stochastic, the time of replication completion cannot be
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THE JOURNAL OF CELL BIOLOGY
Institute of Molecular Genetics, Centre National de la Recherche Scientifique Unité Mixte de Recherche 5535 and University of Montpellier, 34293 Montpellier, France
© 2014 Magiera et al. This article is distributed under the terms of an Attribution–
Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http://www.rupress.org/terms). After six months it is available under a
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as described at http://creativecommons.org/licenses/by-nc-sa/3.0/).
Supplemental Material can be found at:
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Results and discussion
166
Plotting anaphase onset relative to budding normalizes for variability in -factor release kinetics between different strains
and experiments (Fig. 1 B). Using this measure, we found that
anaphase was delayed on average 17 and 12 min in clb5,6 and
SWI5pr-DBF4 cells, respectively (Fig. 1 C). To rule out that this
delay might stem from defects in previous cycles, we expressed
CLB5 conditionally from the tight GALS promoter (Mumberg
et al., 1994) and turned it off before -factor release, which gave
identical results (Fig. S1 A). Thus, delaying S-phase onset by
30 min using independent strategies caused a 15-min delay
in anaphase but no failure in mitosis or cytokinesis. clb5,6 and
SWI5pr-DBF4 cells are enlarged (see Fig. 3 D) but show little
genome instability (Lengronne and Schwob, 2002), suggesting
that ongoing DNA synthesis triggers a checkpoint restraining
mitosis until S phase is completed, after which cells proceed
normally through mitosis.
An explanation for this anaphase delay could be that clb5,6
and SWI5pr-DBF4 cells suffer replication stress, as after deoxynucleotide triphosphate shortage or DNA damage, which slow
S phase. To monitor S-phase kinetics more precisely than by FACS,
we designed a novel assay based on brief ethynyl-deoxyuridine
(EdU) pulses in synchronized cells to visualize ongoing DNA
replication by microscopy (Fig. 1 D). This enabled detection
of S-phase onset and termination and showed that once started,
DNA replication proceeded very similarly in wild-type and
GALS-CLB5 clb6 cells (Fig. 1, E and F), corroborating a previous study (Donaldson et al., 1998). High-resolution SDS-PAGE
and Phos-tag gels also failed to detect Rad53 hyperphosphorylation during S phase in GALS-CLB5 clb6 cells, indicating an
absence of replication stress (Fig. S1 B; Tercero et al., 2003).
Finally, the viability of GALS-CLB5 clb6 and SWI5pr-DBF4
cells did not depend on MEC1, RAD53, or CHK1, in contrast to
cells experiencing replication stress (Fig. S1 C). Together, this
demonstrates that clb5,6 and SWI5pr-DBF4 cells have a replication fingerprint similar to wild-type cells and do not overtly
activate the DNA damage response (DDR). Thus, although
taking place later in the cell cycle, DNA replication in clb5,6
and SWI5pr-DBF4 cells has all the attributes of a physiological
S phase. We conclude that unperturbed DNA replication can
delay chromosome segregation.
Delaying S-phase onset delays
mitotic entry
Ongoing DNA replication delays both G2/M
and anaphase onset
Yeast cells were engineered so to activate their S-phase inducers
S-phase Cdk and DDK later in the cell cycle. Deleting CLB5
and 6 delays S-phase onset by 30 min compared with wild type,
until activation of the next Cdk complex (Clb3,4–Cdk1) compensates for the lack of Clb5,6 (Schwob et al., 1994; Hu and
Aparicio, 2005). Once started, S phase took the same time as in
wild type (Fig. 1 A). To avoid caveats from cyclin deregulation,
we also postponed S phase by expressing DBF4, coding the regulatory subunit of DDK, from the G2-specific SWI5 promoter;
this caused a similar 25–30-min delay without affecting S duration (Fig. 1 A). Strikingly, anaphase determined by the splitting
of tetracycline repressor (TetR)-GFP marked sister chromatids
(Michaelis et al., 1997) culminated at 90–100 min in clb5,6 and
SWI5pr-DBF4 cells, instead of 70–80 min in wild type (Fig. 1 B).
To investigate how DNA replication delays mitosis, we first
monitored M-phase Cdk activation. Clb2–Cdk1 activity measured in vitro or in vivo (Foiani et al., 1995; Liu and Wang, 2006)
was delayed 15–20 min in clb5,6 cells compared with wild type
(Figs. 2 A and S2 A). Because Clb2 and Clb3 accumulate normally (Fig. S2 B), we suspected that Cdc28/Cdk1 was inhibited
by Swe1-dependent phosphorylation on Tyr19. Since SWE1 deletion advances S phase and thus mitosis in clb5,6 cells (Hu and
Aparicio, 2005), we scored anaphase in SWI5pr-DBF4 swe1
and SWI5pr-DBF4 cdc28-F19 cells and found that part of the delay
was suppressed (Fig. 2, B and C). Thus, Swe1-dependent Cdk1
inhibition is partly responsible for the mitotic delay triggered
by ongoing DNA replication, consistent with Swe1 accumulation and Cdc28Tyr19 phosphorylation during unperturbed S phase
JCB • VOLUME 204 • NUMBER 2 • 2014
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predetermined (Hyrien and Goldar, 2010; Rhind et al., 2010).
Hence, it has been assumed that checkpoints monitor either the
presence of unreplicated DNA or DNA synthesis itself and delay
mitosis until all chromosomes are fully copied (Hartwell and
Weinert, 1989; Li and Deshaies, 1993). Yet, cells that fail to
initiate DNA replication nevertheless enter mitosis with little
or no delay, indicating that unreplicated DNA does not prevent
mitosis (Kelly et al., 1993; Piatti et al., 1995).
The dependence of mitosis upon completion of DNA replication has been studied mostly using drugs or mutations that
interfere with replication fork progression. This identified an evolutionarily conserved pathway (Mec1, Ddc2, Chk1, and Rad53
in budding yeast; ATR, ATRIP, Chk1, and Chk2 in mammals),
which is essential for fork stability and cell viability when DNA
replication is perturbed. Cell cycle arrest under these conditions
is caused by accumulation of abnormal DNA structures and excess primed single-strand DNA (Labib et al., 2001; Zou and
Elledge, 2003; Shiotani and Zou, 2009; Van et al., 2010). However, it remains unclear whether this pathway senses normally
progressing forks. The ATR–Chk1–Cdc25A pathway is activated
during unperturbed S phase in cancer cell lines (Sørensen et al.,
2004; Petermann et al., 2006) and during embryogenesis in
mice but not in adult tissues (Murga et al., 2009). Thus, replication stress and checkpoint activation might be constitutive in
rapidly proliferating cells but not in finely tuned somatic cells.
Evidence from yeast also suggests that cells having an extended
S phase can enter mitosis with hyporeplicated DNA without
being detected by checkpoints (Lengronne and Schwob, 2002;
Torres-Rosell et al., 2007; Dulev et al., 2009). Hence, whether
or not an unperturbed S phase elicits a checkpoint capable of
restraining mitotic entry remains an open question. Because
chromosome replication is normally completed before mitosis
begins (Schwob et al., 1994), this question could not be addressed satisfactorily without perturbing S phase. To create a
situation in which chromosomes are still replicating at the time
of normal mitosis, we postponed S-phase onset without affecting its duration and tested whether this delayed S phase was
able, or not, to restrain mitosis.
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Figure 1. Anaphase is delayed when DNA replication is delayed. (A) DNA content after -factor release in wild-type (WT; E1149), clb5 clb6 (E1812),
and SWI5pr-DBF4 (E2011) cells. Black bars, S phase. (B) Sister chromatid separation (two TetR-GFP dots) in the strains above. Arrows, anaphase onset
relative to budding. Representative data from three repeats. (C) tbud-ana calculated from three experiments. (D) Detection of ongoing DNA replication by
EdU pulse labeling. TK-hENT1 yeast cells (E3087) were pulsed for 5 min with EdU, fixed, and processed for tubulin (Tub), DAPI, and EdU detection. DIC,
differential interference contrast. Bar, 5 µm. (E) DNA content of wild-type (E3087) and GALS-CLB5 clb6 cells after -factor release in SC dextrose medium
at 30°C. (F) Ongoing DNA replication in wild-type (E3087) and GALS-CLB5 clb6 (E4495) cells labeled for 5 min with EdU; representative data from two
repeats (n > 100).
Mec1 and Mad2 monitor unperturbed replication • Magiera et al.
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between GALS-CLB5 clb6 cells and DDR mutants. Deletion
of MEC1, RAD9 or introduction of the checkpoint-deficient
mrc1AQ allele had no major effect on the viability of GALSCLB5 clb6 cells grown on glucose, in which S phase is delayed
(Fig. 3 A). A genome-wide synthetic genetic array screen also
failed to reveal synthetic lethality with other DDR components
(unpublished data), indicating that this pathway is either not
involved in the replication-induced anaphase delay or that it
contributes only partially. Indeed, we noticed that GALS-CLB5
clb6 mec1 cells formed smaller colonies on glucose than galactose, suggesting that loss of Mec1 slowed cell division or
caused lethality in a fraction of cells (Fig. 3 A). One explanation
for the viability loss of GALS-CLB5 clb6 mec1 cells could be
that they attempt mitosis before DNA replication is completed.
In fact, GALS-CLB5 clb6 mec1 cells entered anaphase slightly
earlier than GALS-CLB5 clb6 cells (Fig. 3 B), indicating that
the Mec1/ATR checkpoint helps to delay anaphase when DNA
replication is ongoing but is not solely responsible for it.
Securin is stabilized by Mec1-dependent
and -independent mechanisms
(Liu and Wang, 2006). Although Cdc28Tyr19 phosphorylation
was initially ruled out as being responsible for the hydroxy-urea
(HU)–induced arrest in budding yeast (Amon et al., 1992; Sorger
and Murray, 1992), we suggest here that Cdc28Tyr19 inhibition
plays an ancillary role in the coupling of S and M phases under
physiological conditions.
The S-phase checkpoint contributes but is
not essential for the viability of clb5,6 cells
To identify other pathways responsible for the anaphase delay
caused by DNA replication, we looked for synthetic lethality
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Mec1 and Mad2 pathways cooperate
to delay mitosis when DNA replication
is ongoing
Because Pds1 proteolysis was still delayed in GALS-CLB5 clb6
mec1 cells, we suspected that the APCCdc20 was not fully active.
Mad2 is an inhibitor of APCCdc20 and central player of the spindle assembly checkpoint (SAC). Deletion of MAD2 in GALSCLB5 clb6 cells affected their proliferation similarly to MEC1
deletion (Fig. 3 A) and slightly advanced their anaphase onset
(Fig. 3 B). This raised the possibility that Mec1- and Mad2dependent checkpoints independently delay mitosis when DNA
replication is ongoing. If this were the case, disabling both
checkpoints might be lethal for late-replicating cells. Strikingly,
GALS-CLB5 clb6 mec1 mad2 cells grew happily on galactose
plates (normal replication) but produced no colonies on glucose
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Figure 2. Role of Cdc28Y19 in the replication-induced anaphase delay.
(A) In vitro Clb2-associated H1 kinase activity after -factor release in
wild-type (WT; E001) and clb5 clb6 (E145) cells. async, asynchronous.
(B) Anaphase onset in wild-type (E1149), SWI5pr-DBF4 (E2011), SWI5prDBF4 swe1 (E2711), and SWI5pr-DBF4 cdc28Y19F (E2704) cells after
release from -factor. Arrows indicate tbud-ana (n > 100). (C) Relative anaphase timing in the strains indicated above. Experiments were performed
twice and scored independently by two individuals.
As securin proteolysis is key for anaphase onset and a target of
the Mec1–Chk1 pathway, we monitored Pds1 phosphorylation
and proteolysis in GALS-CLB5 clb6 cells, in the presence or
absence of MEC1. Pds1 runs as a doublet on SDS-PAGE during
S and G2 and is degraded in an anaphase-promoting complex
(APC)Cdc20–dependent manner at the meta- to anaphase transition (Cohen-Fix et al., 1996; Agarwal and Cohen-Fix, 2002).
We noticed that the upper band was broader in GALS-CLB5
clb6 cells (suggestive of hyperphosphorylation), and Pds1 was
degraded 15 min later compared with wild type (Fig. 3 C).
The slower migrating band likely corresponds to Pds1 stabilized by Chk1 phosphorylation (Cohen-Fix and Koshland,
1997) because it was lost when MEC1 was deleted. However,
this did not advance Pds1 degradation (Fig. 3 C). We conclude
that (a) Mec1–Chk1 is induced during S phase in GALS-CLB5
clb6 cells yet to a level insufficient to cause the Rad53 hyperphosphorylation seen in HU (Fig. S1 B), and (b) Mec1-dependent
Pds1 phosphorylation is not solely responsible for its tardy degradation when replication is ongoing.
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Figure 3. Deletion of MEC1 and MAD2 is lethal when S phase is delayed. (A) Strains of the indicated genotypes were spotted at serial fivefold dilutions
on YEP plates containing either galactose (Gal) or glucose (Glu) to induce or repress Clb5 synthesis, respectively. (B) Anaphase onset relative to budding
(tbud-ana) was calculated as in Fig. 2 B; values are from two experiments and dual scoring. (C) Western blot of Pds1-myc18 in synchronized wild-type (E686),
mec1 sml1 (E2911), GALS-CLB5 clb6 (E2909), and GALS-CLB5 clb6 mec1 (E2908) cells. Bars indicate S phase measured by FACS (Fig. S2 C). (bottom)
Reloading of the 75-min point; ns, nonspecific band for loading control. Black lines indicate that intervening lanes have been spliced out. (D) Cells were
grown in YEPRG, transferred to YEPD medium, or spotted on YPD plates. Microcolony formation was scored after 24 h (Fig. S3 B), and mean cell volume
was measured 2 and 5 h after shift to YEPD. WT, wild type. div, divisions; cfu, colony-forming unit.
(delayed replication; Fig. 3 A). Thus, MEC1 and MAD2 are essential when S phase occurs late but dispensable if early. Because mec1 mad2 double deletion advanced anaphase further
than mec1 alone (Fig. 3 B), we wondered whether GALS-CLB5
clb6 mec1 mad2 cells died from checkpoint failure followed
by mitotic catastrophe. Indeed most GALS-CLB5 clb6 mec1
mad2 cells died rapidly after shift to glucose, with a cell volume
smaller than the GALS-CLB5 clb6 parent, consistent with escape
from a transient checkpoint arrest (Fig. 3 D). The requirement
of MEC1 and MAD2 for the viability of late-replicating cells
was confirmed in SWI5pr-DBF4 cells, in which genetic analysis
revealed a fourfold lower than expected frequency of SWI5prDBF4 mec1 mad2 progeny (unpublished data). We conclude
that late-replicating cells rely on both the S-phase checkpoint
and the SAC for viability.
The SAC is transiently activated
during S phase
Because it was not anticipated, we explored further the role
of Mad2 and SAC in preventing mitosis while DNA replication is ongoing. MAD1 deletion or expression of the dominant
CDC20-107 allele was also lethal in GALS-CLB5 clb6 mec1
cells (Fig. 4 A), indicating that Mad2 keeps GALS-CLB5 clb6
mec1 cells alive by inhibiting APCCdc20. Mad2 binds monooriented kinetochores, and a single unattached kinetochore is
sufficient to delay mitosis through the SAC (Li and Nicklas,
1995; Chen et al., 1996; Gillett et al., 2004). Of note, kinetochores detach temporarily from microtubules upon centromere
(CEN) replication, consistent with the early and transient SAC
activation seen in unperturbed cell cycles (Brady and Hardwick,
2000; Kitamura et al., 2007). At around the same time, a small
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Figure 4. The SAC is transiently activated during S phase. (A) Viability of GALS-CLB5 clb6 mec1 cells depends on the SAC. Gal, galactose; Glu, glucose.
(B) Mad1 phosphorylation during S phase. Wild-type (WT; E3087) and GALS-CLB5 clb6 (E4495) cells released from G1 were incubated in YEPD 30°C for
the indicated times (in minutes) or 90 min in the presence of 0.2 M HU or 15 µg/ml nocodazole. Cell extracts (10 µg) were resolved on SDS-PAGE (top)
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DNA damage and chromosome loss
in GALS-CLB5 clb6 cells lacking Mec1
and Mad2
Analysis of GALS-CLB5 clb6 mec1 mad2 cells showed that
they entered anaphase with little or no delay, and also exited
mitosis faster than GALS-CLB5 clb6 cells. To see whether this
precipitous mitosis causes DNA damage or double-strand
breaks, we scored Rad52 recombination foci. 150 min after
CLB5 shutoff, 30% of GALS-CLB5 clb6 mec1 mad2 cells contained single or multiple nuclear Rad52 foci compared with 3%
in wild type (Fig. 5 A). When released from G1, wild-type cells
showed Rad52 foci during two successive S phases (45 and
120 min; Fig. 5 B), as expected (Lisby et al., 2001). This wave
of Rad52-positive cells was delayed in GALS-CLB5 clb6 cells,
consistent with their delayed S phase. Deletion of MEC1 increased Rad52 foci in wild-type and GALS-CLB5 clb6 cells, reflecting Mec1’s requirement for fork stability during S phase.
However, the fraction of Rad52 foci increased further in GALSCLB5 clb6 mec1 cells, from 120 min onwards (Fig. 5 B). Deleting MAD2 did not increase further Rad52 foci, despite having
a strong effect on the viability of GALS-CLB5 clb6 mec1 cells.
This could be explained if Mad2 loss caused death of clb5 clb6
mec1 sml1 cells mostly by chromosome missegregation rather
than by increasing DNA damage.
Therefore, we scored the number and position of GFPmarked URA3 loci relative to nuclear morphology. Wild-type
cells showed the expected patterns of tetO/TetR-GFP signals: a
single dot from G1 to metaphase and then splitting of the dots in
early anaphase followed by segregation of the dots to opposite
poles in telophase. We defined four classes of abnormal patterns, as shown in Fig. 5 C. GALS-CLB5 clb6 cells contained
more single dots within an elongating nucleus (nondisjunction),
as expected if anaphase is delayed until replication is completed.
GALS-CLB5 clb6 mec1 cells showed patterns that may correspond to cohesion defects or rearrangements of the tetO array.
MAD2 deletion mainly caused chromosome missegregation with
1:0 or 2:0 patterns. Lastly, deletion of both MEC1 and MAD2
mostly increased chromosome loss events in late-replicating cells
(Fig. 5 C). The high rate of chromosome V loss in GALS-CLB5
clb6 mec1 mad2 cells, extrapolated to the number of yeast chromosomes, most likely accounts for the stark lethality of these
cells. Our observations are corroborated by a recent study that
detected, using a genome-wide approach, a decreased fitness
of clb5 clb6 cells with cohesion and SAC signaling mutants
(Haber et al., 2013).
Mec1 and Mad2 checkpoints are active at
a low level during DNA replication
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fraction of Mad1 gets phosphorylated (Hardwick and Murray,
1995). To see whether this was linked to DNA replication, we
followed Mad1 phosphorylation using Phos-tag gels (Kinoshita
et al., 2006). A fraction of Mad1 shifted 25–45 min after release
in wild type, but this occurred later (40–60 min) in GALS-CLB5
clb6 cells, matching their different replication time (Fig. 4 B).
This S-phase Mad1 phosphorylation is not caused by spindle
assembly stress as initially suggested (Chen et al., 1996), as
bipolar spindles form at the same time in wild-type and clb5,6
cells (Fig. S3 A), yet Mad1 phosphorylation is delayed in the
latter. Rather, we propose that the SAC is activated upon kinetochore disassembly when CENs are duplicated and that this
occurs later when S phase is delayed. Consisten with this idea,
using deconvolution microscopy, we were able to detect Mad2GFP foci proximal to centrosomes (spindle pole bodies [SPBs])
in small budded wild-type cells in S phase but rarely in anaphase and never in unbudded G1 cells. In contrast, Mad2-GFP
foci were seen mostly in large budded GALS-CLB5 clb6 cells
having already separated their SPBs (Fig. 4 C). These results
confirm that spindle formation is uncoupled from DNA replication in budding yeast and strongly suggest that CEN replication
transiently activates the SAC. We propose that delayed CEN duplication prevents anaphase entry through kinetochore detachment causing SAC activation.
The fact that Mec1 and Mad2 each contribute to the viability
and anaphase delay implies that these checkpoints are active in
clb5,6 cells. However, Rad53 is not hyperphosphorylated during S phase in these cells, despite their checkpoint proficiency
(Fig. S1 B). Using Phos-tag gels, we found that Rad53 in fact
exists as three phosphoisoforms in unperturbed wild-type and
clb5 clb6 cells, with a shift toward the higher phosphoforms
during S phase (Fig. S1 B, bottom). Thus, both our genetic and
biochemical evidences indicate that the Mec1–Rad53 pathway
is constitutively active at a low level during S, as suggested previously (Sørensen et al., 2004). Specific structures at normal or
paused replication forks, such as single-strand DNA–replication
protein A complexes, may generate a weak signal for Mec1–
Rad53 activation (Cimprich and Cortez, 2008). Global signal
strength would thus depend on the number of active forks and
would dampen toward the end of S, releasing the brake for mitotic entry. Conversely, CEN replication would generate a transient but potent “wait anaphase” signal, delaying anaphase until
sister kinetochores biorient.
Together, our data demonstrate that the replication checkpoint and SACs are active at a low level during S phase, sufficient to delay anaphase transiently. These signaling pathways,
always active at a low surveillance mode during unperturbed
cell cycles, can be amplified to emergency mode upon extrinsic stress, as witnessed by Rad53 hyperphosphorylation in HU
(Fig. S1 B). Conversely, these anaphase-delaying signals may
fall below threshold after all kinetochores have reassembled
and when the number of active forks drops. This may explain
why yeast mutants completing replication using fewer forks
or Phos-tag gels (bottom). Noc, nocodazole; asterisks, phosphorylated form. FACS is shown in Fig. 1 E. (C) Mad2 localization near SPBs during S phase.
Wild-type (E3536) and GALS-CLB5 clb6 (E3538) diploid cells heterozygous for MAD2-GFP and SPC42-mCherry were grown in SC at 30°C and imaged by
deconvolution microscopy. Mad2 recruitment at kinetochores (arrows) Bars, 5 µm. Quantification indicates percentages of G1, S, metaphase, or anaphase
cells in which Mad2 can be seen as a dot near SPBs. In the remaining cells, Mad2 shows diffuse nuclear staining. DIC, differential interference contrast.
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Figure 5. Chromosome instability in late-replicating cells lacking Mec1 and Mad2. (A) Representative images of asynchronous wild-type (WT; E1925) and
GALS-CLB5 clb6 mec1 mad2 (E2923) cells expressing Rad52-GFP, 150 min after shift to YEPD. The percentage of cells containing Rad52-GFP foci in each
strain is indicated. Bar, 5 µm. (B) Rad52 foci–positive cells after -factor release of wild-type (E2774), GALS-CLB5 clb6 (E2178), GALS-CLB5 clb6 mec1
(E2966), and GALS-CLB5 clb6 mec1 mad2 (E2923) cells; n > 100. (C) Cells of the indicated genotypes (E2288, E2172, E3395, E3397, E3399, and
E3396) were analyzed for abnormal chromosome segregation patterns as indicated in the Materials and methods; n > 100. (D) Model for the cooperation
of Mec1/DDR and Mad2/SAC surveillance mechanisms in monitoring ongoing DNA replication and preventing precocious mitotic entry.
can enter anaphase with incompletely replicated chromosomes
(Lengronne and Schwob, 2002; Torres-Rosell et al., 2007;
Dulev et al., 2009). We propose the following scenario for the
strong synthetic lethality of clb5 clb6 and mec1 mad2 mutants
(Figs. 3 A and 4 A): in clb5 clb6 cells, mitotic entry and anaphase are prevented until replication is completed by the joint
action of Mec1- and Mad2-dependent pathways operating
through signals emanating from ongoing forks and detached
kinetochores, respectively (Fig. 5 D). Mec1 has several roles
beyond signaling replication fork stress, but the contribution
of the latter to the viability of clb5 clb6 mad2 cells is supported by the viability loss conferred by the mrc1-AQ mutation
(Fig. 3 A). Without Mec1, Mad2 signaling is sufficient to sustain viability, and vice versa. However, clb5 clb6 mec1 cells suffer from increased double-strand break/Rad52 foci, perhaps as a
172
JCB • VOLUME 204 • NUMBER 2 • 2014
result of precocious spindle extension or mitosis, and clb5 clb6
mad2 cells show increased chromosome missegregation (Feng
et al., 2009; Haber et al., 2013). In the absence of both Mec1
and Mad2, ongoing replication is not signaled anymore, and
clb5 clb6 cells undergo anaphase before having finished DNA
synthesis and before chromatid biorientation is reestablished.
We suggest that this extreme case of synthetic lethality between
Mec1/DDR and Mad2/SAC inhibition in late-replicating cells
should be explored as a strategy to fight cancer cells that often
show altered replication dynamics.
Checkpoints may have evolved to order
S phase and mitosis in ancestral eukaryotes
Our results show that ongoing DNA synthesis inhibits mitosis
using many of the mechanisms described after replication and
Published January 13, 2014
spindle stresses: Swe1-dependent Cdc28Y19 phosphorylation,
Chk1-induced Pds1/securin stabilization, and Mad2-dependent
APCCdc20 inhibition. When during evolution did these checkpoints arise, and why do they subsist in organisms such as yeast
in which they are dispensable for life? We suggest that the DDR
and SAC evolved in ancestral eukaryotes, when both S phase
and mitosis were set into motion by the same cyclinB–Cdk
complex, and in which mechanisms delaying mitosis until replication is completed were essential to ensure the correct order
of these events (Miranda-Saavedra et al., 2007). It has been shown
that M-phase Cdk can also trigger S phase and that fission yeast
living on a single monomolecular cyclin–Cdk module are highly
dependent on the Wee1 regulatory loop (Moore et al., 2003;
Coudreuse and Nurse, 2010). Checkpoint mechanisms probably
became less important in modern eukaryotes because other
mechanisms, i.e., the temporal separation and specialization of
S-phase and M-phase cyclins, ensured that DNA replication is
finished well before mitosis is attempted. However, their function remained essential to preserve genome integrity when cell
cycle timing controls are overridden (as in this study), after replication stress or in rapid proliferation settings.
Yeast strains and culture
The strains used in this study are listed in Table S1. These strains are congenic or backcrossed at least four times to W303 (MATa ade2-1 trp1-1
can1-100 leu2-3,112 his3-11,15 ura3-1). They were obtained by standard
genetic techniques (Kaiser et al., 1994). The GALS-CLB5 and PDS1-18myc
strains were constructed using published protocols (Longtine et al., 1998;
Janke et al., 2004). The SWI5pr-DBF4 strain was made by integrating the
Apa1-linearized plasmid D1361 at the DBF4 locus. Plasmid D1361 contains
413 bp of the SWI5 promoter fused to a truncated DBF4 gene deleted for
amino acids 333–702 in the YIplac204 vector (Gietz and Sugino, 1988).
Integration generates a truncated dbf4C-ter followed by a full-length
DBF4 driven by the G2/M-specific SWI5 promoter. All strains that indicated
mec1 are also deleted for SML1. CLB2-PrA and CLB3-PrA constructs were
provided by F. Cross (The Rockefeller University, New York, NY), tetO336/
TetR-GFP was provided by K. Nasmyth (Oxford University, Oxford, England, UK), mrc1-AQ was provided by P. Pasero (Institut de Génétique Humaine, Montpellier, France), PDS1-myc18, mad1::LEU2, mad2::URA3,
CDC20-107, and cdc28F19 were provided by S. Piatti (Centre de Recherche de Biochimie Macromoléculaire, Montpellier, France), RAD52-GFP
was provided by R. Rothstein (Columbia University, New York, NY), ADHhENT1 was provided by K. Shirahige (University of Tokyo, Tokyo, Japan),
SPC29-CFP was provided by B. Snydman (Yeast Resource Center, Seattle,
WA), MTW1-4GFP and CTF19-4GFP were provided by T.U. Tanaka (University of Dundee, Dundee, Scotland, UK), and SPC42-mCherry was provided by Y. Watanabe (University of Tokyo, Tokyo, Japan). Unless stated
otherwise, cells were grown in YEP (yeast extract peptone) medium containing 2% glucose (YPD [YEP dextrose]) or 1.8% raffinose and 0.2%
galactose (YPRG). Cell concentration and volume were measured using
the cell counter (CASY1 TTC; Schärfe System).
-Factor release experiments
Cells were grown in YPD to 4 × 106 cell/ml, and 1 µg/ml -factor was
added twice (0 and 75 min) and left for 135 min until release by filtration
or addition of 50 µg/ml pronase (EMD Millipore). Strains containing
GALS-CLB5 were grown in YPRG and shifted to YPD 60 min before release
from -factor.
EdU pulse labeling and detection
GPD-TK ADH-hENT1 cells (E3087) were grown in synthetic complete (SC)
medium, synchronized with -factor, and released in SC medium. Aliquots
were pulsed with 10 µM EdU for 5 min in the same medium, immediately
fixed in 2% PFA, and then permeabilized with 70% EtOH. Cells were incubated in PBS–1% BSA, washed in PBS, resuspended in 50 µl of Click-iT reaction mix containing 2 mM CuSO4, 20 µM DY-530 azide (Dyomics), and
Microscopy
For Rad52-GFP, Mtw1-GFP, and tetO/TetR-GFP detection, cells were grown
in SC medium, centrifuged, resuspended in 10 µl of medium, and fixed by
the addition of 1 ml of 80% ethanol (20°C). For microscopy, 100 µl
of cell suspension was added to 1 ml PBS, briefly sonicated, and concentrated to the desired density. 1.5 µl of cell suspension was put on a
microscope slide and observed using the 100× Plan Apochromat, 1.4 NA
objective on a microscope (DM6000; Leica). Images were acquired with a
camera (CoolSNAP HQ2; Photometrics/Roper Scientific) and MetaMorph
7.6 (Molecular Devices) and then analyzed with ImageJ (National Institutes
of Health). Experiments were performed at least twice, and samples were
number coded and analyzed independently by two people. At least 100 cells
were counted for each time point. The time interval between budding and
anaphase (tbud-ana) was calculated from times at half-maximal budding and
sister chromatid splitting, respectively. Means and SD are indicated. Because tetO repeats are unstable in mec1 strains, we monitored in Fig. 3 B
the segregation of Mtw1-4GFP–marked kinetochores, which cluster as two
close dots (0.8 µm apart) in metaphase and then separate by >4 µm in
anaphase (Joglekar et al., 2009). For Mad2-GFP localization, diploids
containing one MAD2 and one MAD2-GFP allele were grown in SC dextrose medium at 30°C and immediately imaged using a 63× HCX Plan
Apochromat, 1.4 NA objective, 13 z stacks of 0.3 µm, GFP and Cy3 filter
cubes, 300-ms acquisition time, and no binning. The resulting dual-color
images were deconvolved using Huygens Pro (Scientific Volume Imaging)
with the following settings: volume processing, full restoration, supernatant
ratio of 50, background offset of 100%, 20 iterations, quality change
threshold of 0, and output format of 16-bit TIFF. Maximal projections of
deconvolved images were generated with ImageJ and overlaid with the
differential interference contrast image. For chromosome missegregation analysis (Fig. 5 C), cells were grown in YEP medium containing 2%
raffinose and 0.1% galactose, shifted to YPD for 0, 3, or 6 h, stained
with DAPI, and analyzed for abnormal chromosome segregation patterns
according to the following classes: nondisjunction (one dot in extended
nucleus), rearrangements (more than two dots in an extended nucleus),
missegregation (two dots in same nuclear mass), and chromosome loss
(nucleated cell without the CEN V dot).
Downloaded from on June 18, 2017
Materials and methods
10 mM ascorbic acid in PBS, and left for 30 min in the dark. Cells were
washed twice with PBS, incubated 30 min with 0.5 µg/ml DAPI, washed
with PBS, and imaged.
Clb2-associated H1 kinase assay
In brief, 108 cells were washed twice in ice-cold stop mix buffer (150 mM
NaCl, 1 mM NaN3, 10 mM EDTA, and 50 mM NaF), resuspended in
90 µl kinase breakage buffer (KBB; 50 mM Tris-HCl, pH 7.5, 150 mM
NaCl, 15 mM MgCl2, and 1% NP-40 supplemented with proteases and
phosphatases inhibitors), and broken 5 × 30 s with zirconium beads on
a Vibrax at 4°C. Extracts were clarified for 7 min at 12,000 rpm at 4°C,
and protein concentration was measured using a Bradford assay. Clb2 was
immunoprecipitated at 4°C from 100 µg of extract using affinity-purified
anti-Clb2 polyclonal antibodies diluted 1:600 and 15 µl of a 50% protein A–Dynabeads slurry preincubated in KBB + 1 mg/ml BSA. Immune
complexes were diluted in 0.5 ml KBB and washed twice with KBB and
thrice with 25 mM MOPS, pH 7.2, using a magnetic stand. For the kinase
assay, beads were incubated 5 min in 6 µl histone buffer II (25 mM MOPS,
pH 7.5, 15 mM MgCl2, and 5 mM EGTA plus inhibitors) and then 15 min
at 25°C after adding 10 µl kinase buffer (1 mg/ml H1, 25 mM MOPS,
pH 7.2, 100 µM ATP, and 1 µCi -[32P]ATP [3,000 Ci/mmol]).
Whole-cell protein extract from yeast cells
8–20 ml of yeast culture was centrifuged and resuspended in 1 ml of 10%
TCA. Cells were concentrated to 200 µl in 10% TCA, and 200 µl of glass
beads (Zirconia/Silica Beads; BioSpec Products, Inc.) was added. Cells
were then lysed using a FastPrep 120 (Thermo Savant; MP Biomedicals).
Supernatant was transferred to a new tube, the beads were washed twice
with 200 µl of 10% TCA, and extracts were pooled. Extracts were centrifuged
at 3,000 rpm for 10 min, and the pellet was resuspended in 100–200 µl
Laemmli buffer containing 5–10 µl Tris base (1 M). The extracts were boiled
for 5 min, centrifuged for 5 min at 12,000 rpm, and transferred to new
tube. Protein concentration was determined by Bradford assay.
SDS-PAGE and Western blots
10–15 µg whole-cell extracts were run on 8–12% acryl–bisacrylamide
(29:1) gels, except for Rad53 and Mad1 phosphorylation in which 15%
SuperSep Phos-tag gels (Wako Chemicals USA) were used following the
Mec1 and Mad2 monitor unperturbed replication • Magiera et al.
173
Published January 13, 2014
manufacturer’s instructions. Proteins were transferred to nitrocellulose membranes (Protran; Whatman) using wet blotting and revealed using standard
immunoblotting and ECL procedures. Primary antibodies were rabbit polyclonal anti-DNA Pol- B subunit (Pol12; 1:1,000; clone 6D2; gift from
M. Foiani, Italian Foundation for Cancer Research Institute of Molecular
Oncology, Milan, Italy), mouse monoclonal antimyc (1:1,000 from ascites for Pds1-18myc), mouse monoclonal anti-Rad53 (clone EL7; 1:20;
obtained from M. Foiani), and rabbit polyclonal anti-Mad1 (1:3,000; obtained from K. Hardwick, Wellcome Trust, Edinburgh, Scotland, UK).
Online supplemental material
Fig. S1, related to Fig. 1, shows that DNA replication and anaphase are
delayed in the conditional GALS-CLB5 clb6 strain and that Rad53 is neither hyperphosphorylated during the delayed S phase nor required for
the viability of clb5,6 cells. Fig. S2 shows that Clb2 activation is delayed
in vivo despite normal Clb2 protein accumulation (related to Fig. 2 A) and
the FACS profiles for experiments reported in Fig. 3 B. Fig. S3 shows that
bipolar spindles are made at similar times in wild-type and clb5,6 cells
(related to Fig. 1) and terminal phenotype of clb5,6 mec1 mad2 cells (related to Fig. 3, A and D). Table S1 lists the yeast strains used in this study.
Online supplemental material is available at http://www.jcb.org/cgi/
content/full/jcb.201306023/DC1. Additional data are available in the JCB
DataViewer at http://dx.doi.org/10.1083/jcb.201306023.dv.
Submitted: 6 June 2013
Accepted: 9 December 2013
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We dedicate this paper to the memory of our friend and colleague Flavio
Della Seta who prematurely passed away on May 1, 2011.
We thank A. Devault, C. Janke, S. Piatti, and E. Bertrand for critical
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